I've run across this issue, I can't wrap my head around it. I have Windows 7 on a 500GB WD HDD. I decided to upgrade to a SSD, so I bought a SanDisk Extreme Pro 480GB a year and a half ago (somewhere around there). I installed Windows on the SSD, no problems. I left the HDD in there because I was just too lazy to take it out. Every time Windows boots, it boots to the dual boot screen where I choose either the SSD or HDD. I recently bought a 4TB HDD for storage and wanted to get rid of the WD HDD with Windows on it.
First I tried to just format the HDD, which is the D drive. Wouldn't let me do it. I deleted the D drive boot sequence in Windows. Next time I booted the computer, it said "BOOTMGR is missing, press Ctrl+Alt+Delete to restart." I got out the Windows disk and tried to see if I could repair the startup that way. When I clicked on the SSD it said it was running a different version of Windows and this disk couldn't do anything. This is insane and not possible. It's the same disk I used to install Windows on both the SSD and HDD.
Next, I went into the cmd prompt using the recovery disk and tried using bootrec commands. It said Windows Installations: 0, so I couldn't select anything to fix/repair. So, in order to use my SSD, I have to keep the HDD in as the primary boot drive, and then select the SSD when the dual boot menu pops up.
If it helps, this is what comes up when I go into disk management:
SSD (C) Healthy (Boot, Page File, Active, Crash Dump, Primary Partition)
Enterprise (D) Healthy (System, Active, Primary Partition)
First I tried to just format the HDD, which is the D drive. Wouldn't let me do it. I deleted the D drive boot sequence in Windows. Next time I booted the computer, it said "BOOTMGR is missing, press Ctrl+Alt+Delete to restart." I got out the Windows disk and tried to see if I could repair the startup that way. When I clicked on the SSD it said it was running a different version of Windows and this disk couldn't do anything. This is insane and not possible. It's the same disk I used to install Windows on both the SSD and HDD.
Next, I went into the cmd prompt using the recovery disk and tried using bootrec commands. It said Windows Installations: 0, so I couldn't select anything to fix/repair. So, in order to use my SSD, I have to keep the HDD in as the primary boot drive, and then select the SSD when the dual boot menu pops up.
If it helps, this is what comes up when I go into disk management:
SSD (C) Healthy (Boot, Page File, Active, Crash Dump, Primary Partition)
Enterprise (D) Healthy (System, Active, Primary Partition)